chromdyn

A Python library for chromosome dynamics simulation and analysis with options to integrate Hi-C data.

Overview

chromdyn provides tools for building, simulating, and analyzing 3D chromosome structures.
It uses OpenMM for fast CPU/GPU simulations and includes:

• Polymer topology generation
• Customizable force fields
• Hi-C-based restraints
• Simulation utilities
• Analysis tools

Installation

From PyPI

pip install chromdyn

From source (development)

git clone https://github.com/s-brahmachari/chromdyn
cd chromdyn
pip install -e .

Verify Installation

Run the built-in test script:

python -m chromdyn.check_install

Quick Example

from chromdyn import ChromatinDynamics, TopologyGenerator

gen = TopologyGenerator()
gen.gen_top([100])

sim = ChromatinDynamics(
    gen.topology,
    name="demo",
    platform_name="CPU",
)

sim.force_field_manager.add_harmonic_bonds()
sim.simulation_setup(
    init_struct="randomwalk",
    integrator="langevin",
    temperature=300.0,
    timestep=0.01,
)

sim.run(1000)

Tutorials

See the notebooks/ directory for examples on:

• Building polymer models
• Running simulations
• Using Hi-C restraints
• Analyzing trajectories

License

MIT License.